Sunday, February 27, 2011

I read this amusing and instructive story about the dress sense of physicists on a Physics Today blog post by Charles Day:

The most extreme example of sartorial insouciance I've witnessed was that of James Heath, a pioneer of molecular computing (and who would probably call himself a chemist, I should point out).

One November, Heath flew from Los Angeles to Boston to give an invited talk at the Materials Research Society meeting. He showed up in the convention center wearing a brightly colored short-sleeved shirt, shorts, and, if I remember correctly, sandals. Not only had he forgotten to dress for Boston's weather, he'd also left his laptop in California.

Did those mental slips matter? Hardly. Using hastily prepared, hand-written viewgraphs, he gave one of the best talks of the meeting. Indeed, it's conceivable that in creating his viewgraphs, Heath was forced to focus more on his message than on its presentation.

Friday, February 25, 2011

I love the software and book Solid State Simulations. I have used it extensively in teaching, particularly as assignment exercises. I have always been delighted and amazed at how much I have learnt from it too! There is no substitute for visualization. Seeing is believing. I still remember the first time I saw electrons and holes going in opposite directions around their respective Fermi surfaces in a magnetic field.

However, I was alarmed a few weeks ago when I found I could not run it on my Mac. I just started installing a trial version of Parallels to see if it I could run it then. [BTW: I could never get registration for the trial version of VMware Fusion to work]. However, I just discovered that is not necessary! An OSX version has just been released. You can download it for free now.

Thursday, February 24, 2011

Previously I posted about some fascinating experimental results on anisotropic thermal expansion and elastic softening near superconducting and magnetic transitions in organic charge transfer salts.
Subsequently, I became aware that the new iron pnictide superconductors do exhibit somewhat similar phenomena. A combined theory-experimental PRL (10 co-authors!) describes shear acoustic mode spectroscopy in terms of nematic spin fluctuations.

They find in undoped BaFe2As2 that the shear modulus (C66) softens significantly as one approaches the magnetically ordered phase (which is a associated with a tetragonal-orthorhombic lattice distortion). For the optimally doped material there is a hardening of the lattice as one enters the superconducting phase.

The figure above explains the nematic order parameter and how it couples to shear lattice distortions. A key is the that the magnetic phase consists of Neel antiferromagnetic order on two separate sublattices . They are weakly coupled together and the nematic order parameter phi equals the dot product of m1 and m2, the antiferromagnetic order parameters on the two separate lattices. phi then couples directly to the shear strain.

The softening into the superconducting (SC) phase is explained by a coupling of the SC and AFM order parameters. This leads to a change in the static spin susceptibility upon entering the SC phase. This in turn effects the fluctuations in the nematic order parameter.

A couple of comments:

a. Experimental data is presented just for C66. It would be helpful to see it for longitudinal sound and for other transverse modes besides epsilon_s=epsilon_xy. These modes should not have significant coupling to superconductivity and magnetism if the nematic mode is where all the action is.

b. In other antiferromagnets lattice anomalies at magnetic transitions are explained in terms of the spin anisotropy (e.g. due to theDzyaloshinsky-Moriya interaction) coupling to the different components of the stain tensor. This is reviewed here by Lines. Can that be ruled out in the pnictides?

This semester I am co-teaching PHYS4030 Condensed Matter Physics: Electronic properties of crystals. This is a fourth year undergraduate (honours) course. Since there are only 5 students enrolled the course will run as an interactive reading course, somewhat similar to a biophysics course, BIPH3001 and PHYS3170 which I ran the last two years. The text will be the classic Ashcroft and Mermin [Although I wonder if we shouldn't change to Marder].
I have an introductory overview lecture of the first half of the course which discusses 10 key ideas.

Wednesday, February 23, 2011

In the "good old days" university students were "self-motivated", assessment was almost all based on exams and whether students showed up for tutorials and lectures or read the textbook was their own problem. However, the painful reality today is that most students will usually only do some work under a "carrot and stick" system of continuous assessment. Consequently, in many courses students can get credit for just showing up at tutorials and can get easy marks for assignments, some of which they get "help" with from their friends. This means that a student can pass a course even though they get a failing mark on the final exam.

Your overall grade will primarily be determined by the total summative mark. However, you cannot pass the course without also passing the formative component, and an excellent mark for the formative component may push you up into the next highest grade.

The assessment matrix shows the minimum summative mark (along the bottom) and formative mark (down the side) required to achieve each grade:

Tuesday, February 22, 2011

Today there was an interesting Quantum science seminar by Ulrik L. Andersen (Technical University of Denmark) Quantum Plasmonics: Controlled Coupling of a Single Nitrogen-Vacancy Center to a Silver Nanowire.

A question came up about plasmons in gold nano-particles and how the surface plasmon frequency is renormalised downwards (i.e. blue-shifted) compared to the frequency in the bulk. Gerard Milburn pointed out that this is illustrated by The Lycurgus Cup in the British Museum. Coincidentally, an article by Mark Stockman in this months Physics Today states:

The resonant properties of plasmonic metal nanoparticles are readily apparent to the naked eye because the excitations absorb and scatter light at optical frequencies. The most ancient example is the famous fourth-century CE Lycurgus cup from the British museum, whose glass looks green in reflected light but ruby red in transmitted light. Those colors are complementary, evidence that there is little optical loss inside the glass. Investigation has shown that the dichroic glass contains nanocrystals of a gold–silver alloy at a fraction of less than 1%.

Such colloidal suspensions of gold and silver have been widely used in stained glass since the Middle Ages. Transmission through a silver colloid yields yellow light and transmission through gold yields ruby red. The magnificent colored light from the stained glass of the Sainte Chapelle in Paris is assumed to be largely due to the nanoplasmonic resonances.

Unlike glass-staining metal ions such as iron, chromium, copper, and cobalt, metallic nanoparticles, which both absorb and scatter, transmit light with an intensity that strongly depends on the incident and viewing angles. The Sainte Chapelle dramatically exploits the effect: At sunset, the grazing-angle scattering of light by gold nanoparticles in the windows creates a pronounced red glow that appears to slowly move downward, while intensities of blue tints from ions of copper or cobalt remain the same. The artistic impression, probably intended, suggests a stream of blood slowly flowing downward. [See the photo below].

Monday, February 21, 2011

Previously, I posted some notes about an empirical valence bond model for hydrogen bonding.

I have been thinking about whether it is possible to justify such a "simple" picture [and effective Hamiltonian] from high-level quantum chemical calculations. A helpful paper I have been looking at is a 2001 J. Chem. Phys. by Kowal, Roszak, and Leszczynski. They perform complete active space - self-consistent field (CASSCF) calculations on the ground and excited states of the water dimer, (H4O2) and H3O2- and H2O52+. The equilibrium geometry of the latter is pictured below. The three systems correspond to weak, intermediate, and strong hydrogen bonds respectively.

This morning I read slowly read through the paper again. They have 12 electrons in an active space of 7-9 (I think) orbitals, which are localised on the individual atoms.

Below I reproduce the potential energy curves as the O-H bond length with increased with the distance between the oxygen atoms at the equilibrium value.

Notice that in the ground state the potential is very flat (and hence anharmonic).

They also find significant differences in the potential energy surfaces between the three molecular systems they study.

They find that the ground state wavefunction is close to one Slater determinant but usually two determinants are required for the excited states. It is not clear to me why this is? I would have thought that the empirical valence bond (EVB) model would have required two Slater determinants for all the states. Furthermore, the EVB model and the associated four electron-three centre bonding model would suggest that a possibly a four-electron three molecular orbital active space might be sufficient.

This month's issue of Physics Today has a nice article Facilitating science in developing countries about a US based non-profit group Seeding Labs. It was started in 2002 by a few Harvard graduate students to send "out-dated" lab equipment to universities in the developing world.

Sunday, February 20, 2011

Thermoelectric materials are of significant technological interest and present some fundamental scientific questions.
An extremely useful concept is the dimensionless thermoelectric figure of merit. The optimum material with have a high electrical conductivity and thermoelectric power (Seebeck coefficient), but also a low thermal conductivity. This has led to the notion of a Phonon Glass Electron Crystal (PGEC): a material which has the low thermal conductivity characteristic of a glass and the high electrical conductivity characteristic of a crystal. How might one achieve this?
In simple kinetic theory [with well-define acoustic phonon quasi-particles] the thermal conductivity is proportional to the phonon velocity and the phonon mean-free path. In glasses there is so much structural disorder the concept of phonon quasi-particles and a mean-free path is ill defined. In the quasi-particle picture one could reduce the thermal conductivity either by decreasing the phonon mean-free path or by decreasing the phonon speed, or both. The former can happen via a large anharmonicity, which is what is responsible for phonon-phonon scattering. The latter can happen in a soft material or by strongly coupling the acoustic phonons to low frequency optical phonons.

There is a really nice News and Views article Thermoelectrics: Half-full Glasses by Cronin Vingin in Nature Materials that puts in context neutron scattering experiments, on two different classes of materials. [I thank Elvis Shoko for bringing this article to my attention and for helpful discussions]. The first class of materials are clathrates and the second skutterudites. Examples, are methane hydrate and BaFe4Sb12, respectively.

[Aside: previously I posted about superconductivity in skutterudites]. The picture below shows a clathrate structure.

Although, chemically distinct a common structural feature is that both have large cavities within which an atom can "rattle" around in. This means that associated with these motions there are low frequency "optical" phonons which are very anharmonic. These modes then couple to acoustic phonons via coupling to motions of the cage.

The figure is taken from a recent PRB, the introduction to which I found gave a particularly helpful overview.

Thursday, February 17, 2011

A landmark contribution of Linus Pauling was to show the intimate connection between molecular structure and the spatial arrangement of electronic wavefunctions. This is exemplified by the concept of orbital hybridisation. The figure above shows how by taking different linear combinations of s and p orbitals one can produce orbitals with different directionality.

However, as is often the case in quantum chemistry, it turns out not to be quite so simple. I was surprised to learn recently about the notion of imperfect orbital following. Specifically, the direction of the orbitals is not always the same as that of the nuclei, particularly, for non-equilibrium geometries. This can be seen for ammonia as it undergoes the umbrella inversion (the mode associated with the MASER). This phenomenon of orbital following in ammonia was elucidated by Cohan and Coulson in 1956. The figures below are from a JACS paper by Foster and Weinhold. [There is also a nice discussion in the book by Weinhold and Landis.]

In Figure 2 the angle associated with the direction of the orbital is plotted versus the HNH angle in the molecule. If the orbitals followed the nuclear geometry the solid line would lie on top of the dashed line. In the tetrahedral geometry, close to the equilibrium geometry, both angles are about 104 degrees, and the orbitals are approximately sp3. Halfway along the umbrella inversion reaction co-ordinate the molecule has D3 symmetry and both angles are 120 degrees. Roughly the orbitals consist of three sp2 orbitals and a lone pair p orbital.

Tuesday, February 15, 2011

It is amazing and encouraging to me how there are still outstanding problems in science and mathematics that are so simple that statement of the problem can be understood by high school students. An example which has attracted a lot of interest in the past year is the problem of finding the optimum packing efficiency of tetrahedra.
There is a nice New York Times article and a Wolfram blog post about this.

Monday, February 14, 2011

If chemical physicists look ahead with intellectual curiosity to examine the fundamentals of nature, unswayed by fad or funding, I believe that the discipline will be here to stay.

Here are a few other extracts which resonate with me:

opportunities in this century are even more exciting than, and as significant as, in the past, provided that we do not restrict our vision to orthodox boundaries and keep in perspective the core objective of chemical physics.... providing new tools and defining new concepts, but with the lens being focused on significant questions in emerging areas of molecular complexity which span the gamut of applications at the frontiers of chemistry and biology.

Breakthroughs will continue to emerge when applications of visualization methods extend into systems of thousands of atoms and cells, and when the pertinent concepts are generalized with the help of “simple, but not too simple” theories. Computations should be considered as tools, keeping in mind that large-scale computations without a “final” theoretical condensate (or better yet, a “simple equation”) are like large-scale experiments which produce numerous results that do not boil down to a meaningful finding. From both experimental and theoretical studies, the ultimate goal is to provide an understanding of the function from knowledge of structure and dynamics on different length and time scales.

the discipline of chemical physics will become merely a service to other fields only if sight is lost of its primary objective; namely, to provide the fundamental concepts and the new tools that enable understanding and control of the systems behavior, from molecules to cells. The technological benefits will follow, as history has taught us...

He also invokes the image and multi-disciplinarity of the great renaissance painting, The School of Athens, by Raphael, shown above.

Friday, February 11, 2011

The past few weeks I have been puzzling through the implications of some really nice experimental results on superconductivity in organic charge transfer salts. A group at Sherbrooke measured the speed of sound as a function of temperature for different polarisations. The Figure below, taken from their PRB, shows how anisotropic the elastic response is for the material κ-(BEDT-TTF)2Cu[N(CN)2]Br .

The sound is always propagating perpendicular to the layers, which lies in direction of the b axis of the crystal. C22 is the elastic constant for longitudinal sound. C44 has polarisation parallel to the c direction in the crystal which is the same direction as the t' (diagonal) hopping in the relevant Hubbard model [see picture below and this review]. C66 has polarisation in the a direction.

A few thoughts

A really helpful succinct summary of elasticity theory and sound velocity anomalies at Tc is found in Section II of this PRB, also from Sherbrooke [I believe there is an important typo in the expression for the sound velocity in terms of the strain tensor, just below equation (5) the j and k indices on the elastic tensor need to be interchanged.]

These variations in the sound velocity near Tc by about 0.1% may seem small, but they are actually several orders of magnitude larger than in other unconventional superconductors. The authors point this out.

There are fluctuations which extend to temperatures far above Tc. This is consistent with Nernst effect measurements, on the same materials, reported in Nature.

The authors perform an elegant group theoretical argument that forces them to conclude that the anomaly in C66 and other experimental results (STM and thermal conductivity) require that the superconducting order parameter for this crystal must be mixed A1g+B1g

I am not that convinced by the STM and thermal conductivity experiments that claim to determine the locations of the nodes in the energy gap, because these experiments are surface sensitive.

The proposed mixed symmetries are quite inconsistent with many microscopic calculations which predict the order parameter will have B2g symmetry, which competes with A1g near when t'~t and the lattice becomes that of the isotropic triangular lattice, as discussed here. This inconsistency is an important issue that needs to be resolved.

The anisotropic response is somewhat reminiscent of the anisotropy in the thermal expansion near Tc (as shown below) found by Michael Lang's group [see this PRB].

Similar anisotropies and variations in the sound velocity and thermal expansion are also seen near the Mott transition and the crossover from a Fermi liquid to a bad metal.

Thursday, February 10, 2011

O.K. Now I have got your attention, my real point is that just because university paperwork and bureaucracy are often a waste of time does not mean they are always a waste of time. There are several exercises at UQ that I think are particularly valuable and I encourage people to make the most of. They are

Ph.D confirmation documents, seminars, and interviews. This is a "hoop" that students have to jump through after one year of enrolment in order to be allowed to proceed with their Ph.D.

Annual staff performance appraisals.

Some people think these are just another tedious exercise. But, I think both exercises are of great value to all concerned, and are particularly important in cases where performance is poor. Then documentation, due process, and clear communication are important.

With regard to much of the other admin and paperwork, just grit your teeth, tick and complete the boxes, turn it in, and humour the administrators....

Wednesday, February 9, 2011

Many fundamental processes in biology such as signalling and energy conversion make use of the transport and storage of protons within proteins. One widely studied example occurs in vision; in the membrane protein bacteriorhodopsin. Absorption of a photon leads to isomerisation of the retinal molecule which eventually leads to transport of a protein across the cell membrane, resulting in an electrical signal in your nerves.

Hence, a key question concerns the location of the protons at different stages of the process. Generally, high-resolution crystal structures (from X-rays) do not reveal the location of protons.

Over the past decade it has become more appreciated that the location of water molecules inside the protein can provide a key functional role due to their ability to form hydrogen bonds which allow take up and release of protons.

In 2006 a Nature paper by Garczarek and Gerwert used infra-red spectroscopy to investigate the proton dynamics and argued that the water molecules inside the protein were responsible for storing the protons. This picture was supported by a PNAS paper by Mathias and Marx, reporting quantum dynamical calculations which treated the protons at the fully quantum level.

However, a PNAS paper from two years ago [featured in a post two days ago] offers a distinctly different picture. It argues that the proton is shared between oxygen atoms at the carboxylic acid end of the amino acids Glu194 and Glu204.

Glu=glutamine

The carboxylic acid is the C-OOH group at the lower right

So what do I learn from all this?

there are still fundamental problems in molecular biology which are still waiting to be solved [and some of them involve quantum dynamics!]

one needs to be very careful in the interpretation of experiments and calculations. This is why the method of multiple hypotheses are so important.

Monday, February 7, 2011

Sorry! nLA= n-letter acronym
If you want to attract an audience to attend your talk, read your paper, and/or like your grant application, I would encourage you not to use acronym's (e.g., EPR, DFT, SA-CAS-SCF, DMFT, NOON, ADMR, etc.). The chances are most of the people not working on exactly the same topic will have no idea what you are talking about. If so, they will quickly lose interest and possibly resent being immediately excluded.

The Figure above is taken from a fascinating PNAS paper which I will post about later on. But this post is just to point out an important point illustrated by the Figure. It shows the location of different amino acids (Glu194, Ser193, etc..) inside the protein bacteriorhodopsin. Each different colour corresponds to the location determined and published by a different experimental group. To a physicist the differences look pretty minor. However, it turns out the exact distance between the oxygen atoms at the end of the Glu194 and Glu204 residues turn out to be crucial for understanding where proton involved in the protein-pump function of the protein is stored.
A second more general point is that the different structures illustrate that one should always take published protein crystal structures with a healthy skepticism.

Saturday, February 5, 2011

What are the really key ingredients to important research breakthroughs? Is the involvement of commercial interests helpful, neutral, or a hindrance?The following letter appeared in the Sydney Morning Herald last month. I read it when it was reprinted in The Week. This was in the context of an article Doctors criticise leukemia drug study concerning potential conflicts of interest.

Drug companies are not a cure-all

Stephen Mulligan (Letters, January 26) says: "Collaboration between leading clinicians and industry, under appropriate guidelines, is not just desirable but essential. Without it there will be no progress in clinical research, and the textbooks for treatment for 2050 and beyond could be written now."

Really? Two of the greatest medical advances in the past 50 years, both identified primarily by Australians, were the discoveries of the causal relationship of some types of papilloma viruses to cancer of the cervix and that of Helicobacter pylori to peptic ulcer (the latter gaining a Nobel Prize for its discoverers).

Neither required the intervention of drug companies, or of umpteen authors, or even much research money, just the sheer genius of insight - insights overlooked by the rest of us for years.

Thursday, February 3, 2011

In 1995 Phil Anderson organised a colloquium: "Physics: the opening to complexity" for the USA National Academy of Sciences. His introduction is worth reading. I reproduce below an extract because it gives such a clear discussion of emergence.

At this frontier [of complexity], the watchword is not reductionism but emergence. Emergent complex phenomena are by no means in violation of the microscopic laws, but they do not appear as logicaly consequent on these laws. That this is the case can be illustrated by two examples which show that a complex phenomenon can follow laws independently of the detailed substrate in which it is expressed.

(i) The "Bardeen-Cooper-Schrieffer (BCS)" phenomenon of broken gauge symmetry in dense Fermion liquids has at least three expressions: electrons in metals, of course, where it is called "superconductivity"; 3He atoms, which become a superfluid when liquid 3He is cooled below 1-3 mK; and nucleons both in ordinary nuclei (the pairing phenomenon explained by Bohr, Mottelson, and Pines) and in neutron stars, on a giant scale, where superfluidity is responsible for the "glitch" phenomenon. All of these different physical embodients obey the general laws of broken symmetry that are the canonical example of emergence in physics.

(ii) One may make a digital computer using electrical relays, vacuum tubes, transistors, or neurons; .... the rules governing computation do not vary depending on the physical substrate in which they are expressed; hence, they are logically independent of the physical laws governing that substrate.

Wednesday, February 2, 2011

I just read a really helpful paper Optical symmetries and anisotropic transport in high-Tc transport by Tom Devereaux. Although the paper is a PRB it reads more like a short review. It is very clear and provides lots of summary expressions. The main purpose of the paper is to show the intimate connection between low-frequency electronic Raman scattering and charge conductivity. [n.b. this Raman scattering is NOT scattering off phonons but electron-hole pairs]. Furthermore, intra-layer and inter-layer conductivity can be related to Raman scattering of different symmetries [A1g, B1g, B2g]. The figure below shows this correlation.

I was particularly interested in the paper for several reasons:

It is possible to define scattering rates associated with the electronic scattering and to relate these to scattering on the Fermi surface in the nodal and anti-nodal directions. This allows a comparison to be made with the temperature dependence predicted by "cold spot", "hot spot", and marginal Fermi liquid models for the anisotropy in the scattering rate.

I am hoping someone will do Raman experiments on organic charge transfer salts and see if they can see the anisotropic superconducting gap and possibly an anisotropic pseudogap

The expressions given could be used to calculate how the Raman response changes as there is a crossover from a bad medal to a Fermi liquid in a DMFT treatment of the Hubbard model.

The momentum dependence of the interlayer hopping [it vanishes in the nodal directions] is crucial for differences to occur between A1g and B1g scattering.

It is pointed out that the derived results for the A1g Raman and interlayer conductivity require that the intralayer momentum is conserved [at least partially] for interlayer hopping. This same condition is necessary for the observation of angle-dependent interlayer magnetoresistance, as discussed here.

Tuesday, February 1, 2011

Being a referee is somewhat of a thankless task. It means being a good citizen and putting the interests of the scientific community before your own. Furthermore, if you are conscientious and provide a helpful report in a timely manner, the journal editors will "reward" you by sending you more and more papers to referee. Postdocs can easily sink a lot of time into refereeing papers, to little personal gain. Someone once told me a helpful rule for being a good scientific citizen: you should referee approximately the same number of papers per year as you submit [normalised to the number of co-authors]. I encourage my postdocs to follow this guideline.

Some good reasons to referee a paper:

You have some constructive feedback that will improve the paper.

The paper has serious flaws.

It is good experience to learn how referee's may respond to your papers.

Some good reasons to not referee a paper:

You are too busy and can't provide a report in a timely manner.

You can't be objective because of a conflict of interest.

You already referee more than your share of papers [see the rule above].

You already have one paper to referee.

You really don't have the expertise to evaluate the validity and/or importance of the paper.

The paper is so poorly written it is difficult to follow.

Some bad reasons to referee a paper:

You just can't say no.

You mistakenly think that if you say no the journal editors won't be sympathetic to your next submission.

The paper is from a competitor and you want to stop it getting published.

You mistakenly think that being a referee looks particularly good on your CV.

The paper cites a least one of your papers and so you want it to be published.

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About Me

I have fun at work trying to use quantum many-body theory to understand electronic properties of complex materials.
I am married to the lovely Robin and have two adult children and a dog, Priya (in the photo). I also write an even more personal blog Soli Deo Gloria [thoughts on theology, science, and culture]

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Although I am employed by the University of Queensland and funded by the Australian Research Council all views expressed on this blog are solely my own. They do not reflect the views of any present or past employers, funding agencies, colleagues, organisations, family members, churches, insurance companies, or lawyers I currently have or in the past have had some affiliation with.

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